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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 435 by mmeineke, Fri Mar 28 19:33:37 2003 UTC vs.
Revision 859 by mmeineke, Mon Nov 10 21:50:36 2003 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTxyz_ENS     4
25	+
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33		SimSetup::SimSetup(){
34	+
35	+	initSuspend = false;
36	+	isInfoArray = 0;
37	+	nInfo = 1;
38	+
39		stamps = new MakeStamps();
40		globals = new Globals();
41	<
41	>
42	>
43		#ifdef IS_MPI
44	<	strcpy( checkPointMsg, "SimSetup creation successful" );
44	>	strcpy(checkPointMsg, "SimSetup creation successful");
45		MPIcheckPoint();
46		#endif // IS_MPI
47		}
#	Line 27 | Line 51 | void SimSetup::parseFile( char* fileName ){
51		delete globals;
52		}
53
54	<	void SimSetup::parseFile( char* fileName ){
54	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
55	>	info = the_info;
56	>	nInfo = theNinfo;
57	>	isInfoArray = 1;
58	>	initSuspend = true;
59	>	}
60
61	+
62	+	void SimSetup::parseFile(char* fileName){
63		#ifdef IS_MPI
64	<	if( worldRank == 0 ){
64	>	if (worldRank == 0){
65		#endif // is_mpi
66	<
66	>
67		inFileName = fileName;
68	<	set_interface_stamps( stamps, globals );
69	<
68	>	set_interface_stamps(stamps, globals);
69	>
70		#ifdef IS_MPI
71		mpiEventInit();
72		#endif
73
74	<	yacc_BASS( fileName );
74	>	yacc_BASS(fileName);
75
76		#ifdef IS_MPI
77		throwMPIEvent(NULL);
78		}
79	<	else receiveParse();
79	>	else{
80	>	receiveParse();
81	>	}
82		#endif
83
84		}
85
86		#ifdef IS_MPI
87		void SimSetup::receiveParse(void){
88	<
89	<	set_interface_stamps( stamps, globals );
90	<	mpiEventInit();
91	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
88	>	set_interface_stamps(stamps, globals);
89	>	mpiEventInit();
90	>	MPIcheckPoint();
91	>	mpiEventLoop();
92		}
93
94		#endif // is_mpi
95
96	<	void SimSetup::createSim( void ){
96	>	void SimSetup::createSim(void){
97
98	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
98	>	// gather all of the information from the Bass file
99
100	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
100	>	gatherInfo();
101
102	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
102	>	// creation of complex system objects
103
104	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
104	>	sysObjectsCreation();
105
106	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
106	>	// check on the post processing info
107
108	+	finalInfoCheck();
109
110	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
92	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93	<	else{
94	<	sprintf( painCave.errMsg,
95	<	"SimSetup Error. Unrecognized force field -> %s\n",
96	<	force_field );
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
110	>	// initialize the system coordinates
111
112	<	#ifdef IS_MPI
113	<	strcpy( checkPointMsg, "ForceField creation successful" );
103	<	MPIcheckPoint();
104	<	#endif // is_mpi
112	>	if ( !initSuspend ){
113	>	initSystemCoords();
114
115	<
115	>	if( !(globals->getUseInitTime()) )
116	>	info[0].currentTime = 0.0;
117	>	}
118
119	<	// get the components and calculate the tot_nMol and indvidual n_mol
109	<	the_components = the_globals->getComponents();
110	<	components_nmol = new int[n_components];
111	<	comp_stamps = new MoleculeStamp*[n_components];
119	>	// make the output filenames
120
121	<	if( !the_globals->haveNMol() ){
114	<	// we don't have the total number of molecules, so we assume it is
115	<	// given in each component
121	>	makeOutNames();
122
123	<	tot_nmol = 0;
118	<	for( i=0; i<n_components; i++ ){
123	>	// make the integrator
124
125	<	if( !the_components[i]->haveNMol() ){
121	<	// we have a problem
122	<	sprintf( painCave.errMsg,
123	<	"SimSetup Error. No global NMol or component NMol"
124	<	" given. Cannot calculate the number of atoms.\n" );
125	<	painCave.isFatal = 1;
126	<	simError();
127	<	}
125	>	makeIntegrator();
126
129	–	tot_nmol += the_components[i]->getNMol();
130	–	components_nmol[i] = the_components[i]->getNMol();
131	–	}
132	–	}
133	–	else{
134	–	sprintf( painCave.errMsg,
135	–	"SimSetup error.\n"
136	–	"\tSorry, the ability to specify total"
137	–	" nMols and then give molfractions in the components\n"
138	–	"\tis not currently supported."
139	–	" Please give nMol in the components.\n" );
140	–	painCave.isFatal = 1;
141	–	simError();
142	–
143	–
144	–	//     tot_nmol = the_globals->getNMol();
145	–
146	–	//   //we have the total number of molecules, now we check for molfractions
147	–	//     for( i=0; i<n_components; i++ ){
148	–
149	–	//       if( !the_components[i]->haveMolFraction() ){
150	–
151	–	//  if( !the_components[i]->haveNMol() ){
152	–	//    //we have a problem
153	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
154	–	//              << " nMol was given in component
155	–
156	–	}
157	–
127		#ifdef IS_MPI
128	<	strcpy( checkPointMsg, "Have the number of components" );
129	<	MPIcheckPoint();
161	<	#endif // is_mpi
128	>	mpiSim->mpiRefresh();
129	>	#endif
130
131	<	// make an array of molecule stamps that match the components used.
164	<	// also extract the used stamps out into a separate linked list
131	>	// initialize the Fortran
132
133	<	simnfo->nComponents = n_components;
134	<	simnfo->componentsNmol = components_nmol;
168	<	simnfo->compStamps = comp_stamps;
169	<	simnfo->headStamp = new LinkedMolStamp();
170	<
171	<	char* id;
172	<	LinkedMolStamp* headStamp = simnfo->headStamp;
173	<	LinkedMolStamp* currentStamp = NULL;
174	<	for( i=0; i<n_components; i++ ){
133	>	initFortran();
134	>	}
135
176	–	id = the_components[i]->getType();
177	–	comp_stamps[i] = NULL;
178	–
179	–	// check to make sure the component isn't already in the list
136
137	<	comp_stamps[i] = headStamp->match( id );
138	<	if( comp_stamps[i] == NULL ){
139	<
140	<	// extract the component from the list;
141	<
142	<	currentStamp = the_stamps->extractMolStamp( id );
143	<	if( currentStamp == NULL ){
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup error: Component \"%s\" was not found in the "
146	<	"list of declared molecules\n",
147	<	id );
192	<	painCave.isFatal = 1;
193	<	simError();
194	<	}
195	<
196	<	headStamp->add( currentStamp );
197	<	comp_stamps[i] = headStamp->match( id );
198	<	}
199	<	}
137	>	void SimSetup::makeMolecules(void){
138	>	int k;
139	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	>	molInit molInfo;
141	>	DirectionalAtom* dAtom;
142	>	LinkedAssign* extras;
143	>	LinkedAssign* current_extra;
144	>	AtomStamp* currentAtom;
145	>	BondStamp* currentBond;
146	>	BendStamp* currentBend;
147	>	TorsionStamp* currentTorsion;
148
149	<	#ifdef IS_MPI
150	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
151	<	MPIcheckPoint();
204	<	#endif // is_mpi
205	<
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
153
154	+	//init the forceField paramters
155
156	<	// caclulate the number of atoms, bonds, bends and torsions
156	>	the_ff->readParams();
157
211	–	tot_atoms = 0;
212	–	tot_bonds = 0;
213	–	tot_bends = 0;
214	–	tot_torsions = 0;
215	–	for( i=0; i<n_components; i++ ){
216	–
217	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221	–	}
158
159	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
159	>	// init the atoms
160
161	<	simnfo->n_atoms = tot_atoms;
226	<	simnfo->n_bonds = tot_bonds;
227	<	simnfo->n_bends = tot_bends;
228	<	simnfo->n_torsions = tot_torsions;
229	<	simnfo->n_SRI = tot_SRI;
230	<	simnfo->n_mol = tot_nmol;
161	>	double ux, uy, uz, u, uSqr;
162
163	<
164	<	#ifdef IS_MPI
163	>	for (k = 0; k < nInfo; k++){
164	>	the_ff->setSimInfo(&(info[k]));
165
166	<	// divide the molecules among processors here.
167	<
168	<	mpiSim = new mpiSimulation( simnfo );
169	<
239	<
166	>	atomOffset = 0;
167	>	excludeOffset = 0;
168	>	for (i = 0; i < info[k].n_mol; i++){
169	>	stampID = info[k].molecules[i].getStampID();
170
171	<	globalIndex = mpiSim->divideLabor();
171	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
172	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
173	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
174	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
175	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
176
177	<	// set up the local variables
178	<
179	<	int localMol, allMol;
180	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
177	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
178	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
179	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
180	>	molInfo.myBends = new Bend * [molInfo.nBends];
181	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
182
183	<	int* mol2proc = mpiSim->getMolToProcMap();
184	<	int* molCompType = mpiSim->getMolComponentType();
185	<
251	<	allMol = 0;
252	<	localMol = 0;
253	<	local_atoms = 0;
254	<	local_bonds = 0;
255	<	local_bends = 0;
256	<	local_torsions = 0;
257	<	for( i=0; i<n_components; i++ ){
183	>	theBonds = new bond_pair[molInfo.nBonds];
184	>	theBends = new bend_set[molInfo.nBends];
185	>	theTorsions = new torsion_set[molInfo.nTorsions];
186
187	<	for( j=0; j<components_nmol[i]; j++ ){
260	<
261	<	if( mol2proc[j] == worldRank ){
262	<
263	<	local_atoms +=    comp_stamps[i]->getNAtoms();
264	<	local_bonds +=    comp_stamps[i]->getNBonds();
265	<	local_bends +=    comp_stamps[i]->getNBends();
266	<	local_torsions += comp_stamps[i]->getNTorsions();
267	<	localMol++;
268	<	}
269	<	allMol++;
270	<	}
271	<	}
272	<	local_SRI = local_bonds + local_bends + local_torsions;
273	<
187	>	// make the Atoms
188
189	<	simnfo->n_atoms = mpiSim->getMyNlocal();
190	<
191	<	if( local_atoms != simnfo->n_atoms ){
192	<	sprintf( painCave.errMsg,
193	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
194	<	" localAtom (%d) are not equal.\n",
195	<	simnfo->n_atoms,
282	<	local_atoms );
283	<	painCave.isFatal = 1;
284	<	simError();
285	<	}
189	>	for (j = 0; j < molInfo.nAtoms; j++){
190	>	currentAtom = comp_stamps[stampID]->getAtom(j);
191	>	if (currentAtom->haveOrientation()){
192	>	dAtom = new DirectionalAtom((j + atomOffset),
193	>	info[k].getConfiguration());
194	>	info[k].n_oriented++;
195	>	molInfo.myAtoms[j] = dAtom;
196
197	<	simnfo->n_bonds = local_bonds;
198	<	simnfo->n_bends = local_bends;
199	<	simnfo->n_torsions = local_torsions;
290	<	simnfo->n_SRI = local_SRI;
291	<	simnfo->n_mol = localMol;
197	>	ux = currentAtom->getOrntX();
198	>	uy = currentAtom->getOrntY();
199	>	uz = currentAtom->getOrntZ();
200
201	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
294	<	MPIcheckPoint();
295	<
296	<
297	<	#endif // is_mpi
298	<
201	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202
203	<	// create the atom and short range interaction arrays
203	>	u = sqrt(uSqr);
204	>	ux = ux / u;
205	>	uy = uy / u;
206	>	uz = uz / u;
207
208	<	Atom::createArrays(simnfo->n_atoms);
209	<	the_atoms = new Atom*[simnfo->n_atoms];
210	<	the_molecules = new Molecule[simnfo->n_mol];
211	<	int molIndex;
208	>	dAtom->setSUx(ux);
209	>	dAtom->setSUy(uy);
210	>	dAtom->setSUz(uz);
211	>	}
212	>	else{
213	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
214	>	info[k].getConfiguration());
215	>	}
216	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
217
307	–	// initialize the molecule's stampID's
308	–
218		#ifdef IS_MPI
310	–
219
220	<	molIndex = 0;
313	<	for(i=0; i<mpiSim->getTotNmol(); i++){
314	<
315	<	if(mol2proc[i] == worldRank ){
316	<	the_molecules[molIndex].setStampID( molCompType[i] );
317	<	molIndex++;
318	<	}
319	<	}
220	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
221
321	–	#else // is_mpi
322	–
323	–	molIndex = 0;
324	–	for(i=0; i<n_components; i++){
325	–	for(j=0; j<components_nmol[i]; j++ ){
326	–	the_molecules[molIndex].setStampID( i );
327	–	molIndex++;
328	–	}
329	–	}
330	–
331	–
222		#endif // is_mpi
223	+	}
224
225	+	// make the bonds
226	+	for (j = 0; j < molInfo.nBonds; j++){
227	+	currentBond = comp_stamps[stampID]->getBond(j);
228	+	theBonds[j].a = currentBond->getA() + atomOffset;
229	+	theBonds[j].b = currentBond->getB() + atomOffset;
230
231	<	if( simnfo->n_SRI ){
232	<
337	<	std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
338	<
339	<	Exclude::createArray(simnfo->n_SRI);
340	<	the_excludes = new Exclude*[simnfo->n_SRI];
341	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
342	<	simnfo->globalExcludes = new int;
343	<	simnfo->n_exclude = tot_SRI;
344	<	}
345	<	else{
346	<
347	<	Exclude::createArray( 1 );
348	<	the_excludes = new Exclude*;
349	<	the_excludes[0] = new Exclude(0);
350	<	the_excludes[0]->setPair( 0,0 );
351	<	simnfo->globalExcludes = new int;
352	<	simnfo->globalExcludes[0] = 0;
353	<	simnfo->n_exclude = 0;
354	<	}
231	>	exI = theBonds[j].a;
232	>	exJ = theBonds[j].b;
233
234	<	// set the arrays into the SimInfo object
234	>	// exclude_I must always be the smaller of the pair
235	>	if (exI > exJ){
236	>	tempEx = exI;
237	>	exI = exJ;
238	>	exJ = tempEx;
239	>	}
240	>	#ifdef IS_MPI
241	>	tempEx = exI;
242	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	>	tempEx = exJ;
244	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
245
246	<	simnfo->atoms = the_atoms;
247	<	simnfo->molecules = the_molecules;
360	<	simnfo->nGlobalExcludes = 0;
361	<	simnfo->excludes = the_excludes;
246	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247	>	#else  // isn't MPI
248
249	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250	+	#endif  //is_mpi
251	+	}
252	+	excludeOffset += molInfo.nBonds;
253
254	<	// get some of the tricky things that may still be in the globals
254	>	//make the bends
255	>	for (j = 0; j < molInfo.nBends; j++){
256	>	currentBend = comp_stamps[stampID]->getBend(j);
257	>	theBends[j].a = currentBend->getA() + atomOffset;
258	>	theBends[j].b = currentBend->getB() + atomOffset;
259	>	theBends[j].c = currentBend->getC() + atomOffset;
260
261	<
262	<	if( the_globals->haveBox() ){
263	<	simnfo->box_x = the_globals->getBox();
369	<	simnfo->box_y = the_globals->getBox();
370	<	simnfo->box_z = the_globals->getBox();
371	<	}
372	<	else if( the_globals->haveDensity() ){
261	>	if (currentBend->haveExtras()){
262	>	extras = currentBend->getExtras();
263	>	current_extra = extras;
264
265	<	double vol;
266	<	vol = (double)tot_nmol / the_globals->getDensity();
267	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
268	<	simnfo->box_y = simnfo->box_x;
269	<	simnfo->box_z = simnfo->box_x;
270	<	}
271	<	else{
381	<	if( !the_globals->haveBoxX() ){
382	<	sprintf( painCave.errMsg,
383	<	"SimSetup error, no periodic BoxX size given.\n" );
384	<	painCave.isFatal = 1;
385	<	simError();
386	<	}
387	<	simnfo->box_x = the_globals->getBoxX();
265	>	while (current_extra != NULL){
266	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
267	>	switch (current_extra->getType()){
268	>	case 0:
269	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272
273	<	if( !the_globals->haveBoxY() ){
274	<	sprintf( painCave.errMsg,
275	<	"SimSetup error, no periodic BoxY size given.\n" );
276	<	painCave.isFatal = 1;
277	<	simError();
394	<	}
395	<	simnfo->box_y = the_globals->getBoxY();
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278
279	<	if( !the_globals->haveBoxZ() ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error, no periodic BoxZ size given.\n" );
282	<	painCave.isFatal = 1;
283	<	simError();
284	<	}
285	<	simnfo->box_z = the_globals->getBoxZ();
286	<	}
279	>	default:
280	>	sprintf(painCave.errMsg,
281	>	"SimSetup Error: ghostVectorSource was neither a "
282	>	"double nor an int.\n"
283	>	"-->Bend[%d] in %s\n",
284	>	j, comp_stamps[stampID]->getID());
285	>	painCave.isFatal = 1;
286	>	simError();
287	>	}
288	>	}
289	>	else{
290	>	sprintf(painCave.errMsg,
291	>	"SimSetup Error: unhandled bend assignment:\n"
292	>	"    -->%s in Bend[%d] in %s\n",
293	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297
298	+	current_extra = current_extra->getNext();
299	+	}
300	+	}
301	+
302	+	if (!theBends[j].isGhost){
303	+	exI = theBends[j].a;
304	+	exJ = theBends[j].c;
305	+	}
306	+	else{
307	+	exI = theBends[j].a;
308	+	exJ = theBends[j].b;
309	+	}
310	+
311	+	// exclude_I must always be the smaller of the pair
312	+	if (exI > exJ){
313	+	tempEx = exI;
314	+	exI = exJ;
315	+	exJ = tempEx;
316	+	}
317		#ifdef IS_MPI
318	<	strcpy( checkPointMsg, "Box size set up" );
319	<	MPIcheckPoint();
320	<	#endif // is_mpi
318	>	tempEx = exI;
319	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	>	tempEx = exJ;
321	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
322
323	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
324	+	#else  // isn't MPI
325	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
326	+	#endif  //is_mpi
327	+	}
328	+	excludeOffset += molInfo.nBends;
329
330	<	// initialize the arrays
330	>	for (j = 0; j < molInfo.nTorsions; j++){
331	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
332	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
333	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
334	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
335	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
336
337	<	the_ff->setSimInfo( simnfo );
337	>	exI = theTorsions[j].a;
338	>	exJ = theTorsions[j].d;
339
340	<	makeMolecules();
341	<	simnfo->identArray = new int[simnfo->n_atoms];
342	<	for(i=0; i<simnfo->n_atoms; i++){
343	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
344	<	}
345	<
346	<	if (the_globals->getUseRF() ) {
347	<	simnfo->useReactionField = 1;
348	<
349	<	if( !the_globals->haveECR() ){
350	<	sprintf( painCave.errMsg,
427	<	"SimSetup Warning: using default value of 1/2 the smallest "
428	<	"box length for the electrostaticCutoffRadius.\n"
429	<	"I hope you have a very fast processor!\n");
430	<	painCave.isFatal = 0;
431	<	simError();
432	<	double smallest;
433	<	smallest = simnfo->box_x;
434	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
435	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
436	<	simnfo->ecr = 0.5 * smallest;
437	<	} else {
438	<	simnfo->ecr        = the_globals->getECR();
439	<	}
340	>	// exclude_I must always be the smaller of the pair
341	>	if (exI > exJ){
342	>	tempEx = exI;
343	>	exI = exJ;
344	>	exJ = tempEx;
345	>	}
346	>	#ifdef IS_MPI
347	>	tempEx = exI;
348	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349	>	tempEx = exJ;
350	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351
352	<	if( !the_globals->haveEST() ){
353	<	sprintf( painCave.errMsg,
354	<	"SimSetup Warning: using default value of 0.05 * the "
355	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
445	<	);
446	<	painCave.isFatal = 0;
447	<	simError();
448	<	simnfo->est = 0.05 * simnfo->ecr;
449	<	} else {
450	<	simnfo->est        = the_globals->getEST();
451	<	}
452	<
453	<	if(!the_globals->haveDielectric() ){
454	<	sprintf( painCave.errMsg,
455	<	"SimSetup Error: You are trying to use Reaction Field without"
456	<	"setting a dielectric constant!\n"
457	<	);
458	<	painCave.isFatal = 1;
459	<	simError();
460	<	}
461	<	simnfo->dielectric = the_globals->getDielectric();
462	<	} else {
463	<	if (simnfo->n_dipoles) {
464	<
465	<	if( !the_globals->haveECR() ){
466	<	sprintf( painCave.errMsg,
467	<	"SimSetup Warning: using default value of 1/2 the smallest"
468	<	"box length for the electrostaticCutoffRadius.\n"
469	<	"I hope you have a very fast processor!\n");
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	double smallest;
473	<	smallest = simnfo->box_x;
474	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
475	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
476	<	simnfo->ecr = 0.5 * smallest;
477	<	} else {
478	<	simnfo->ecr        = the_globals->getECR();
352	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
353	>	#else  // isn't MPI
354	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
355	>	#endif  //is_mpi
356		}
357	<
358	<	if( !the_globals->haveEST() ){
359	<	sprintf( painCave.errMsg,
360	<	"SimSetup Warning: using default value of 5% of the"
361	<	"electrostaticCutoffRadius for the "
362	<	"electrostaticSkinThickness\n"
363	<	);
364	<	painCave.isFatal = 0;
365	<	simError();
366	<	simnfo->est = 0.05 * simnfo->ecr;
367	<	} else {
368	<	simnfo->est        = the_globals->getEST();
369	<	}
357	>	excludeOffset += molInfo.nTorsions;
358	>
359	>
360	>	// send the arrays off to the forceField for init.
361	>
362	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
363	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
364	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
365	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
366	>	theTorsions);
367	>
368	>
369	>	info[k].molecules[i].initialize(molInfo);
370	>
371	>
372	>	atomOffset += molInfo.nAtoms;
373	>	delete[] theBonds;
374	>	delete[] theBends;
375	>	delete[] theTorsions;
376		}
377	<	}
377	>	}
378
379		#ifdef IS_MPI
380	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
380	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
381		MPIcheckPoint();
382		#endif // is_mpi
383
384	<	if( the_globals->haveInitialConfig() ){
502	<
503	<	InitializeFromFile* fileInit;
504	<	#ifdef IS_MPI // is_mpi
505	<	if( worldRank == 0 ){
506	<	#endif //is_mpi
507	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
508	<	#ifdef IS_MPI
509	<	}else fileInit = new InitializeFromFile( NULL );
510	<	#endif
511	<	fileInit->read_xyz( simnfo ); // default velocities on
384	>	// clean up the forcefield
385
386	<	delete fileInit;
387	<	}
388	<	else{
386	>	the_ff->calcRcut();
387	>	the_ff->cleanMe();
388	>	}
389
390	<	#ifdef IS_MPI
390	>	void SimSetup::initFromBass(void){
391	>	int i, j, k;
392	>	int n_cells;
393	>	double cellx, celly, cellz;
394	>	double temp1, temp2, temp3;
395	>	int n_per_extra;
396	>	int n_extra;
397	>	int have_extra, done;
398
399	<	// no init from bass
400	<
401	<	sprintf( painCave.errMsg,
402	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
523	<	painCave.isFatal;
524	<	simError();
525	<
526	<	#else
399	>	double vel[3];
400	>	vel[0] = 0.0;
401	>	vel[1] = 0.0;
402	>	vel[2] = 0.0;
403
404	<	initFromBass();
404	>	temp1 = (double) tot_nmol / 4.0;
405	>	temp2 = pow(temp1, (1.0 / 3.0));
406	>	temp3 = ceil(temp2);
407
408	+	have_extra = 0;
409	+	if (temp2 < temp3){
410	+	// we have a non-complete lattice
411	+	have_extra = 1;
412
413	<	#endif
414	<	}
413	>	n_cells = (int) temp3 - 1;
414	>	cellx = info[0].boxL[0] / temp3;
415	>	celly = info[0].boxL[1] / temp3;
416	>	cellz = info[0].boxL[2] / temp3;
417	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
418	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
419	>	n_per_extra = (int) ceil(temp1);
420
421	<	#ifdef IS_MPI
422	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
423	<	MPIcheckPoint();
424	<	#endif // is_mpi
421	>	if (n_per_extra > 4){
422	>	sprintf(painCave.errMsg,
423	>	"SimSetup error. There has been an error in constructing"
424	>	" the non-complete lattice.\n");
425	>	painCave.isFatal = 1;
426	>	simError();
427	>	}
428	>	}
429	>	else{
430	>	n_cells = (int) temp3;
431	>	cellx = info[0].boxL[0] / temp3;
432	>	celly = info[0].boxL[1] / temp3;
433	>	cellz = info[0].boxL[2] / temp3;
434	>	}
435
436	+	current_mol = 0;
437	+	current_comp_mol = 0;
438	+	current_comp = 0;
439	+	current_atom_ndx = 0;
440
441	<
442	<
443	<
441	>	for (i = 0; i < n_cells ; i++){
442	>	for (j = 0; j < n_cells; j++){
443	>	for (k = 0; k < n_cells; k++){
444	>	makeElement(i * cellx, j * celly, k * cellz);
445
446	<
447	<	#ifdef IS_MPI
448	<	if( worldRank == 0 ){
449	<	#endif // is_mpi
450	<
549	<	if( the_globals->haveFinalConfig() ){
550	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
551	<	}
552	<	else{
553	<	strcpy( simnfo->finalName, inFileName );
554	<	char* endTest;
555	<	int nameLength = strlen( simnfo->finalName );
556	<	endTest = &(simnfo->finalName[nameLength - 5]);
557	<	if( !strcmp( endTest, ".bass" ) ){
558	<	strcpy( endTest, ".eor" );
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
447	>
448	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
449	>
450	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
451		}
560	–	else if( !strcmp( endTest, ".BASS" ) ){
561	–	strcpy( endTest, ".eor" );
562	–	}
563	–	else{
564	–	endTest = &(simnfo->finalName[nameLength - 4]);
565	–	if( !strcmp( endTest, ".bss" ) ){
566	–	strcpy( endTest, ".eor" );
567	–	}
568	–	else if( !strcmp( endTest, ".mdl" ) ){
569	–	strcpy( endTest, ".eor" );
570	–	}
571	–	else{
572	–	strcat( simnfo->finalName, ".eor" );
573	–	}
574	–	}
452		}
453	<
454	<	// make the sample and status out names
455	<
456	<	strcpy( simnfo->sampleName, inFileName );
457	<	char* endTest;
458	<	int nameLength = strlen( simnfo->sampleName );
459	<	endTest = &(simnfo->sampleName[nameLength - 5]);
460	<	if( !strcmp( endTest, ".bass" ) ){
461	<	strcpy( endTest, ".dump" );
462	<	}
463	<	else if( !strcmp( endTest, ".BASS" ) ){
464	<	strcpy( endTest, ".dump" );
465	<	}
466	<	else{
467	<	endTest = &(simnfo->sampleName[nameLength - 4]);
468	<	if( !strcmp( endTest, ".bss" ) ){
469	<	strcpy( endTest, ".dump" );
470	<	}
471	<	else if( !strcmp( endTest, ".mdl" ) ){
472	<	strcpy( endTest, ".dump" );
473	<	}
474	<	else{
475	<	strcat( simnfo->sampleName, ".dump" );
453	>	}
454	>
455	>	if (have_extra){
456	>	done = 0;
457	>
458	>	int start_ndx;
459	>	for (i = 0; i < (n_cells + 1) && !done; i++){
460	>	for (j = 0; j < (n_cells + 1) && !done; j++){
461	>	if (i < n_cells){
462	>	if (j < n_cells){
463	>	start_ndx = n_cells;
464	>	}
465	>	else
466	>	start_ndx = 0;
467	>	}
468	>	else
469	>	start_ndx = 0;
470	>
471	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
472	>	makeElement(i * cellx, j * celly, k * cellz);
473	>	done = (current_mol >= tot_nmol);
474	>
475	>	if (!done && n_per_extra > 1){
476	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
477	>	k * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480	>
481	>	if (!done && n_per_extra > 2){
482	>	makeElement(i * cellx, j * celly + 0.5 * celly,
483	>	k * cellz + 0.5 * cellz);
484	>	done = (current_mol >= tot_nmol);
485	>	}
486	>
487	>	if (!done && n_per_extra > 3){
488	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
489	>	k * cellz + 0.5 * cellz);
490	>	done = (current_mol >= tot_nmol);
491	>	}
492	>	}
493		}
494		}
601	–
602	–	strcpy( simnfo->statusName, inFileName );
603	–	nameLength = strlen( simnfo->statusName );
604	–	endTest = &(simnfo->statusName[nameLength - 5]);
605	–	if( !strcmp( endTest, ".bass" ) ){
606	–	strcpy( endTest, ".stat" );
607	–	}
608	–	else if( !strcmp( endTest, ".BASS" ) ){
609	–	strcpy( endTest, ".stat" );
610	–	}
611	–	else{
612	–	endTest = &(simnfo->statusName[nameLength - 4]);
613	–	if( !strcmp( endTest, ".bss" ) ){
614	–	strcpy( endTest, ".stat" );
615	–	}
616	–	else if( !strcmp( endTest, ".mdl" ) ){
617	–	strcpy( endTest, ".stat" );
618	–	}
619	–	else{
620	–	strcat( simnfo->statusName, ".stat" );
621	–	}
622	–	}
623	–
624	–	#ifdef IS_MPI
495		}
626	–	#endif // is_mpi
627	–
628	–	// set the status, sample, and themal kick times
629	–
630	–	if( the_globals->haveSampleTime() ){
631	–	simnfo->sampleTime = the_globals->getSampleTime();
632	–	simnfo->statusTime = simnfo->sampleTime;
633	–	simnfo->thermalTime = simnfo->sampleTime;
634	–	}
635	–	else{
636	–	simnfo->sampleTime = the_globals->getRunTime();
637	–	simnfo->statusTime = simnfo->sampleTime;
638	–	simnfo->thermalTime = simnfo->sampleTime;
639	–	}
496
497	<	if( the_globals->haveStatusTime() ){
498	<	simnfo->statusTime = the_globals->getStatusTime();
497	>	for (i = 0; i < info[0].n_atoms; i++){
498	>	info[0].atoms[i]->setVel(vel);
499		}
500	+	}
501
502	<	if( the_globals->haveThermalTime() ){
503	<	simnfo->thermalTime = the_globals->getThermalTime();
504	<	}
502	>	void SimSetup::makeElement(double x, double y, double z){
503	>	int k;
504	>	AtomStamp* current_atom;
505	>	DirectionalAtom* dAtom;
506	>	double rotMat[3][3];
507	>	double pos[3];
508
509	<	// check for the temperature set flag
509	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
510	>	current_atom = comp_stamps[current_comp]->getAtom(k);
511	>	if (!current_atom->havePosition()){
512	>	sprintf(painCave.errMsg,
513	>	"SimSetup:initFromBass error.\n"
514	>	"\tComponent %s, atom %s does not have a position specified.\n"
515	>	"\tThe initialization routine is unable to give a start"
516	>	" position.\n",
517	>	comp_stamps[current_comp]->getID(), current_atom->getType());
518	>	painCave.isFatal = 1;
519	>	simError();
520	>	}
521
522	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
522	>	pos[0] = x + current_atom->getPosX();
523	>	pos[1] = y + current_atom->getPosY();
524	>	pos[2] = z + current_atom->getPosZ();
525
526	+	info[0].atoms[current_atom_ndx]->setPos(pos);
527
528	<	//   // make the longe range forces and the integrator
528	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
529	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
530
531	<	//   new AllLong( simnfo );
531	>	rotMat[0][0] = 1.0;
532	>	rotMat[0][1] = 0.0;
533	>	rotMat[0][2] = 0.0;
534
535	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
536	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
535	>	rotMat[1][0] = 0.0;
536	>	rotMat[1][1] = 1.0;
537	>	rotMat[1][2] = 0.0;
538
539	<	#ifdef IS_MPI
540	<	mpiSim->mpiRefresh();
541	<	#endif
539	>	rotMat[2][0] = 0.0;
540	>	rotMat[2][1] = 0.0;
541	>	rotMat[2][2] = 1.0;
542
543	<	// initialize the Fortran
543	>	dAtom->setA(rotMat);
544	>	}
545
546	<
668	<	simnfo->refreshSim();
669	<
670	<	if( !strcmp( simnfo->mixingRule, "standard") ){
671	<	the_ff->initForceField( LB_MIXING_RULE );
546	>	current_atom_ndx++;
547		}
673	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
674	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
675	–	}
676	–	else{
677	–	sprintf( painCave.errMsg,
678	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
679	–	simnfo->mixingRule );
680	–	painCave.isFatal = 1;
681	–	simError();
682	–	}
548
549	+	current_mol++;
550	+	current_comp_mol++;
551
552	<	#ifdef IS_MPI
553	<	strcpy( checkPointMsg,
554	<	"Successfully intialized the mixingRule for Fortran." );
555	<	MPIcheckPoint();
689	<	#endif // is_mpi
552	>	if (current_comp_mol >= components_nmol[current_comp]){
553	>	current_comp_mol = 0;
554	>	current_comp++;
555	>	}
556		}
557
558
559	<	void SimSetup::makeMolecules( void ){
559	>	void SimSetup::gatherInfo(void){
560	>	int i;
561
562	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
563	<	molInit info;
697	<	DirectionalAtom* dAtom;
698	<	LinkedAssign* extras;
699	<	LinkedAssign* current_extra;
700	<	AtomStamp* currentAtom;
701	<	BondStamp* currentBond;
702	<	BendStamp* currentBend;
703	<	TorsionStamp* currentTorsion;
562	>	ensembleCase = -1;
563	>	ffCase = -1;
564
565	<	bond_pair* theBonds;
706	<	bend_set* theBends;
707	<	torsion_set* theTorsions;
565	>	// set the easy ones first
566
567	<
568	<	//init the forceField paramters
567	>	for (i = 0; i < nInfo; i++){
568	>	info[i].target_temp = globals->getTargetTemp();
569	>	info[i].dt = globals->getDt();
570	>	info[i].run_time = globals->getRunTime();
571	>	}
572	>	n_components = globals->getNComponents();
573
712	–	the_ff->readParams();
574
575	<
715	<	// init the atoms
575	>	// get the forceField
576
577	<	double ux, uy, uz, u, uSqr;
718	<
719	<	atomOffset = 0;
720	<	excludeOffset = 0;
721	<	for(i=0; i<simnfo->n_mol; i++){
722	<
723	<	stampID = the_molecules[i].getStampID();
577	>	strcpy(force_field, globals->getForceField());
578
579	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
580	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
581	<	info.nBends    = comp_stamps[stampID]->getNBends();
582	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
583	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
579	>	if (!strcasecmp(force_field, "DUFF")){
580	>	ffCase = FF_DUFF;
581	>	}
582	>	else if (!strcasecmp(force_field, "LJ")){
583	>	ffCase = FF_LJ;
584	>	}
585	>	else if (!strcasecmp(force_field, "EAM")){
586	>	ffCase = FF_EAM;
587	>	}
588	>	else{
589	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
590	>	force_field);
591	>	painCave.isFatal = 1;
592	>	simError();
593	>	}
594
595	<	info.myAtoms = &the_atoms[atomOffset];
732	<	info.myExcludes = &the_excludes[excludeOffset];
733	<	info.myBonds = new Bond*[info.nBonds];
734	<	info.myBends = new Bend*[info.nBends];
735	<	info.myTorsions = new Torsion*[info.nTorsions];
595	>	// get the ensemble
596
597	<	theBonds = new bond_pair[info.nBonds];
738	<	theBends = new bend_set[info.nBends];
739	<	theTorsions = new torsion_set[info.nTorsions];
740	<
741	<	// make the Atoms
742	<
743	<	for(j=0; j<info.nAtoms; j++){
744	<
745	<	currentAtom = comp_stamps[stampID]->getAtom( j );
746	<	if( currentAtom->haveOrientation() ){
747	<
748	<	dAtom = new DirectionalAtom(j + atomOffset);
749	<	simnfo->n_oriented++;
750	<	info.myAtoms[j] = dAtom;
751	<
752	<	ux = currentAtom->getOrntX();
753	<	uy = currentAtom->getOrntY();
754	<	uz = currentAtom->getOrntZ();
755	<
756	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
757	<
758	<	u = sqrt( uSqr );
759	<	ux = ux / u;
760	<	uy = uy / u;
761	<	uz = uz / u;
762	<
763	<	dAtom->setSUx( ux );
764	<	dAtom->setSUy( uy );
765	<	dAtom->setSUz( uz );
766	<	}
767	<	else{
768	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
769	<	}
770	<	info.myAtoms[j]->setType( currentAtom->getType() );
771	<
772	<	#ifdef IS_MPI
773	<
774	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
775	<
776	<	#endif // is_mpi
777	<	}
778	<
779	<	// make the bonds
780	<	for(j=0; j<info.nBonds; j++){
781	<
782	<	currentBond = comp_stamps[stampID]->getBond( j );
783	<	theBonds[j].a = currentBond->getA() + atomOffset;
784	<	theBonds[j].b = currentBond->getB() + atomOffset;
597	>	strcpy(ensemble, globals->getEnsemble());
598
599	<	exI = theBonds[j].a;
600	<	exJ = theBonds[j].b;
599	>	if (!strcasecmp(ensemble, "NVE")){
600	>	ensembleCase = NVE_ENS;
601	>	}
602	>	else if (!strcasecmp(ensemble, "NVT")){
603	>	ensembleCase = NVT_ENS;
604	>	}
605	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
606	>	ensembleCase = NPTi_ENS;
607	>	}
608	>	else if (!strcasecmp(ensemble, "NPTf")){
609	>	ensembleCase = NPTf_ENS;
610	>	}
611	>	else if (!strcasecmp(ensemble, "NPTxyz")){
612	>	ensembleCase = NPTxyz_ENS;
613	>	}
614	>	else{
615	>	sprintf(painCave.errMsg,
616	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
617	>	"reverting to NVE for this simulation.\n",
618	>	ensemble);
619	>	painCave.isFatal = 0;
620	>	simError();
621	>	strcpy(ensemble, "NVE");
622	>	ensembleCase = NVE_ENS;
623	>	}
624
625	<	// exclude_I must always be the smaller of the pair
626	<	if( exI > exJ ){
791	<	tempEx = exI;
792	<	exI = exJ;
793	<	exJ = tempEx;
794	<	}
795	<	#ifdef IS_MPI
796	<	tempEx = exI;
797	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
798	<	tempEx = exJ;
799	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
800	<
801	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
802	<	#else  // isn't MPI
625	>	for (i = 0; i < nInfo; i++){
626	>	strcpy(info[i].ensemble, ensemble);
627
628	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
805	<	#endif  //is_mpi
806	<	}
807	<	excludeOffset += info.nBonds;
628	>	// get the mixing rule
629
630	<	//make the bends
631	<	for(j=0; j<info.nBends; j++){
632	<
812	<	currentBend = comp_stamps[stampID]->getBend( j );
813	<	theBends[j].a = currentBend->getA() + atomOffset;
814	<	theBends[j].b = currentBend->getB() + atomOffset;
815	<	theBends[j].c = currentBend->getC() + atomOffset;
816	<
817	<	if( currentBend->haveExtras() ){
818	<
819	<	extras = currentBend->getExtras();
820	<	current_extra = extras;
821	<
822	<	while( current_extra != NULL ){
823	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
824	<
825	<	switch( current_extra->getType() ){
826	<
827	<	case 0:
828	<	theBends[j].ghost =
829	<	current_extra->getInt() + atomOffset;
830	<	theBends[j].isGhost = 1;
831	<	break;
832	<
833	<	case 1:
834	<	theBends[j].ghost =
835	<	(int)current_extra->getDouble() + atomOffset;
836	<	theBends[j].isGhost = 1;
837	<	break;
838	<
839	<	default:
840	<	sprintf( painCave.errMsg,
841	<	"SimSetup Error: ghostVectorSource was neither a "
842	<	"double nor an int.\n"
843	<	"-->Bend[%d] in %s\n",
844	<	j, comp_stamps[stampID]->getID() );
845	<	painCave.isFatal = 1;
846	<	simError();
847	<	}
848	<	}
849	<
850	<	else{
851	<
852	<	sprintf( painCave.errMsg,
853	<	"SimSetup Error: unhandled bend assignment:\n"
854	<	"    -->%s in Bend[%d] in %s\n",
855	<	current_extra->getlhs(),
856	<	j, comp_stamps[stampID]->getID() );
857	<	painCave.isFatal = 1;
858	<	simError();
859	<	}
860	<
861	<	current_extra = current_extra->getNext();
862	<	}
863	<	}
864	<
865	<	if( !theBends[j].isGhost ){
866	<
867	<	exI = theBends[j].a;
868	<	exJ = theBends[j].c;
869	<	}
870	<	else{
871	<
872	<	exI = theBends[j].a;
873	<	exJ = theBends[j].b;
874	<	}
875	<
876	<	// exclude_I must always be the smaller of the pair
877	<	if( exI > exJ ){
878	<	tempEx = exI;
879	<	exI = exJ;
880	<	exJ = tempEx;
881	<	}
882	<	#ifdef IS_MPI
883	<	tempEx = exI;
884	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
885	<	tempEx = exJ;
886	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
887	<
888	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
889	<	#else  // isn't MPI
890	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
891	<	#endif  //is_mpi
892	<	}
893	<	excludeOffset += info.nBends;
630	>	strcpy(info[i].mixingRule, globals->getMixingRule());
631	>	info[i].usePBC = globals->getPBC();
632	>	}
633
634	<	for(j=0; j<info.nTorsions; j++){
896	<
897	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
898	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
899	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
900	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
901	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
902	<
903	<	exI = theTorsions[j].a;
904	<	exJ = theTorsions[j].d;
634	>	// get the components and calculate the tot_nMol and indvidual n_mol
635
636	<	// exclude_I must always be the smaller of the pair
637	<	if( exI > exJ ){
908	<	tempEx = exI;
909	<	exI = exJ;
910	<	exJ = tempEx;
911	<	}
912	<	#ifdef IS_MPI
913	<	tempEx = exI;
914	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
915	<	tempEx = exJ;
916	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
917	<
918	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
919	<	#else  // isn't MPI
920	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
921	<	#endif  //is_mpi
922	<	}
923	<	excludeOffset += info.nTorsions;
636	>	the_components = globals->getComponents();
637	>	components_nmol = new int[n_components];
638
925	–
926	–	// send the arrays off to the forceField for init.
639
640	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
641	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
642	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
931	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
640	>	if (!globals->haveNMol()){
641	>	// we don't have the total number of molecules, so we assume it is
642	>	// given in each component
643
644	+	tot_nmol = 0;
645	+	for (i = 0; i < n_components; i++){
646	+	if (!the_components[i]->haveNMol()){
647	+	// we have a problem
648	+	sprintf(painCave.errMsg,
649	+	"SimSetup Error. No global NMol or component NMol"
650	+	" given. Cannot calculate the number of atoms.\n");
651	+	painCave.isFatal = 1;
652	+	simError();
653	+	}
654
655	<	the_molecules[i].initialize( info );
656	<	atomOffset += info.nAtoms;
657	<	delete[] theBonds;
937	<	delete[] theBends;
938	<	delete[] theTorsions;
655	>	tot_nmol += the_components[i]->getNMol();
656	>	components_nmol[i] = the_components[i]->getNMol();
657	>	}
658		}
659	+	else{
660	+	sprintf(painCave.errMsg,
661	+	"SimSetup error.\n"
662	+	"\tSorry, the ability to specify total"
663	+	" nMols and then give molfractions in the components\n"
664	+	"\tis not currently supported."
665	+	" Please give nMol in the components.\n");
666	+	painCave.isFatal = 1;
667	+	simError();
668	+	}
669
670	<	#ifdef IS_MPI
942	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
943	<	MPIcheckPoint();
944	<	#endif // is_mpi
670	>	// set the status, sample, and thermal kick times
671
672	<	// clean up the forcefield
673	<	the_ff->calcRcut();
674	<	the_ff->cleanMe();
672	>	for (i = 0; i < nInfo; i++){
673	>	if (globals->haveSampleTime()){
674	>	info[i].sampleTime = globals->getSampleTime();
675	>	info[i].statusTime = info[i].sampleTime;
676	>	info[i].thermalTime = info[i].sampleTime;
677	>	}
678	>	else{
679	>	info[i].sampleTime = globals->getRunTime();
680	>	info[i].statusTime = info[i].sampleTime;
681	>	info[i].thermalTime = info[i].sampleTime;
682	>	}
683
684	<	}
684	>	if (globals->haveStatusTime()){
685	>	info[i].statusTime = globals->getStatusTime();
686	>	}
687
688	<	void SimSetup::initFromBass( void ){
688	>	if (globals->haveThermalTime()){
689	>	info[i].thermalTime = globals->getThermalTime();
690	>	}
691
692	<	int i, j, k;
693	<	int n_cells;
694	<	double cellx, celly, cellz;
695	<	double temp1, temp2, temp3;
696	<	int n_per_extra;
959	<	int n_extra;
960	<	int have_extra, done;
692	>	info[i].resetIntegrator = 0;
693	>	if( globals->haveResetTime() ){
694	>	info[i].resetTime = globals->getResetTime();
695	>	info[i].resetIntegrator = 1;
696	>	}
697
698	<	temp1 = (double)tot_nmol / 4.0;
699	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
700	<	temp3 = ceil( temp2 );
698	>	// check for the temperature set flag
699	>
700	>	if (globals->haveTempSet())
701	>	info[i].setTemp = globals->getTempSet();
702
703	<	have_extra =0;
967	<	if( temp2 < temp3 ){ // we have a non-complete lattice
968	<	have_extra =1;
703	>	// check for the extended State init
704
705	<	n_cells = (int)temp3 - 1;
706	<	cellx = simnfo->box_x / temp3;
707	<	celly = simnfo->box_y / temp3;
708	<	cellz = simnfo->box_z / temp3;
709	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
710	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
711	<	n_per_extra = (int)ceil( temp1 );
705	>	info[i].useInitXSstate = globals->getUseInitXSstate();
706	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
707	>
708	>	}
709	>
710	>	//setup seed for random number generator
711	>	int seedValue;
712
713	<	if( n_per_extra > 4){
714	<	sprintf( painCave.errMsg,
715	<	"SimSetup error. There has been an error in constructing"
716	<	" the non-complete lattice.\n" );
717	<	painCave.isFatal = 1;
713	>	if (globals->haveSeed()){
714	>	seedValue = globals->getSeed();
715	>
716	>	if(seedValue / 1E9 == 0){
717	>	sprintf(painCave.errMsg,
718	>	"Seed for sprng library should contain at least 9 digits\n"
719	>	"OOPSE will generate a seed for user\n");
720	>	painCave.isFatal = 0;
721		simError();
722	<	}
723	<	}
722	>
723	>	//using seed generated by system instead of invalid seed set by user
724	>	#ifndef IS_MPI
725	>	seedValue = make_sprng_seed();
726	>	#else
727	>	if (worldRank == 0){
728	>	seedValue = make_sprng_seed();
729	>	}
730	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
731	>	#endif
732	>	}
733	>	}//end of if branch of globals->haveSeed()
734		else{
735	<	n_cells = (int)temp3;
736	<	cellx = simnfo->box_x / temp3;
737	<	celly = simnfo->box_y / temp3;
738	<	cellz = simnfo->box_z / temp3;
735	>
736	>	#ifndef IS_MPI
737	>	seedValue = make_sprng_seed();
738	>	#else
739	>	if (worldRank == 0){
740	>	seedValue = make_sprng_seed();
741	>	}
742	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
743	>	#endif
744	>	}//end of globals->haveSeed()
745	>
746	>	for (int i = 0; i < nInfo; i++){
747	>	info[i].setSeed(seedValue);
748		}
749
750	<	current_mol = 0;
751	<	current_comp_mol = 0;
752	<	current_comp = 0;
753	<	current_atom_ndx = 0;
750	>	#ifdef IS_MPI
751	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
752	>	MPIcheckPoint();
753	>	#endif // is_mpi
754	>	}
755
998	–	for( i=0; i < n_cells ; i++ ){
999	–	for( j=0; j < n_cells; j++ ){
1000	–	for( k=0; k < n_cells; k++ ){
756
757	<	makeElement( i * cellx,
758	<	j * celly,
759	<	k * cellz );
757	>	void SimSetup::finalInfoCheck(void){
758	>	int index;
759	>	int usesDipoles;
760	>	int i;
761
762	<	makeElement( i * cellx + 0.5 * cellx,
763	<	j * celly + 0.5 * celly,
1008	<	k * cellz );
762	>	for (i = 0; i < nInfo; i++){
763	>	// check electrostatic parameters
764
765	<	makeElement( i * cellx,
766	<	j * celly + 0.5 * celly,
767	<	k * cellz + 0.5 * cellz );
765	>	index = 0;
766	>	usesDipoles = 0;
767	>	while ((index < info[i].n_atoms) && !usesDipoles){
768	>	usesDipoles = (info[i].atoms[index])->hasDipole();
769	>	index++;
770	>	}
771
772	<	makeElement( i * cellx + 0.5 * cellx,
773	<	j * celly,
774	<	k * cellz + 0.5 * cellz );
772	>	#ifdef IS_MPI
773	>	int myUse = usesDipoles;
774	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
775	>	#endif //is_mpi
776	>
777	>	double theEcr, theEst;
778	>
779	>	if (globals->getUseRF()){
780	>	info[i].useReactionField = 1;
781	>
782	>	if (!globals->haveECR()){
783	>	sprintf(painCave.errMsg,
784	>	"SimSetup Warning: using default value of 15.0 angstroms"
785	>	"box length for the electrostaticCutoffRadius.\n");
786	>	painCave.isFatal = 0;
787	>	simError();
788	>	theEcr = 15.0;
789		}
790	+	else{
791	+	theEcr = globals->getECR();
792	+	}
793	+
794	+	if (!globals->haveEST()){
795	+	sprintf(painCave.errMsg,
796	+	"SimSetup Warning: using default value of 0.05 * the "
797	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
798	+	painCave.isFatal = 0;
799	+	simError();
800	+	theEst = 0.05 * theEcr;
801	+	}
802	+	else{
803	+	theEst = globals->getEST();
804	+	}
805	+
806	+	info[i].setDefaultEcr(theEcr, theEst);
807	+
808	+	if (!globals->haveDielectric()){
809	+	sprintf(painCave.errMsg,
810	+	"SimSetup Error: You are trying to use Reaction Field without"
811	+	"setting a dielectric constant!\n");
812	+	painCave.isFatal = 1;
813	+	simError();
814	+	}
815	+	info[i].dielectric = globals->getDielectric();
816		}
817	+	else{
818	+	if (usesDipoles){
819	+	if (!globals->haveECR()){
820	+	sprintf(painCave.errMsg,
821	+	"SimSetup Warning: using default value of 15.0 angstroms"
822	+	"box length for the electrostaticCutoffRadius.\n");
823	+	painCave.isFatal = 0;
824	+	simError();
825	+	theEcr = 15.0;
826	+	}
827	+	else{
828	+	theEcr = globals->getECR();
829	+	}
830	+
831	+	if (!globals->haveEST()){
832	+	sprintf(painCave.errMsg,
833	+	"SimSetup Warning: using default value of 0.05 * the "
834	+	"electrostaticCutoffRadius for the "
835	+	"electrostaticSkinThickness\n");
836	+	painCave.isFatal = 0;
837	+	simError();
838	+	theEst = 0.05 * theEcr;
839	+	}
840	+	else{
841	+	theEst = globals->getEST();
842	+	}
843	+
844	+	info[i].setDefaultEcr(theEcr, theEst);
845	+	}
846	+	}
847		}
848	+	#ifdef IS_MPI
849	+	strcpy(checkPointMsg, "post processing checks out");
850	+	MPIcheckPoint();
851	+	#endif // is_mpi
852	+	}
853	+
854	+	void SimSetup::initSystemCoords(void){
855	+	int i;
856
857	<	if( have_extra ){
1022	<	done = 0;
857	>	char* inName;
858
859	<	int start_ndx;
1025	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1026	<	for( j=0; j < (n_cells+1) && !done; j++ ){
859	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
860
861	<	if( i < n_cells ){
861	>	for (i = 0; i < info[0].n_atoms; i++)
862	>	info[0].atoms[i]->setCoords();
863
864	<	if( j < n_cells ){
865	<	start_ndx = n_cells;
866	<	}
867	<	else start_ndx = 0;
868	<	}
869	<	else start_ndx = 0;
864	>	if (globals->haveInitialConfig()){
865	>	InitializeFromFile* fileInit;
866	>	#ifdef IS_MPI // is_mpi
867	>	if (worldRank == 0){
868	>	#endif //is_mpi
869	>	inName = globals->getInitialConfig();
870	>	fileInit = new InitializeFromFile(inName);
871	>	#ifdef IS_MPI
872	>	}
873	>	else
874	>	fileInit = new InitializeFromFile(NULL);
875	>	#endif
876	>	fileInit->readInit(info); // default velocities on
877
878	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
878	>	delete fileInit;
879	>	}
880	>	else{
881	>
882	>	// no init from bass
883	>
884	>	sprintf(painCave.errMsg,
885	>	"Cannot intialize a simulation without an initial configuration file.\n");
886	>	painCave.isFatal = 1;;
887	>	simError();
888	>
889	>	}
890
891	<	makeElement( i * cellx,
892	<	j * celly,
893	<	k * cellz );
894	<	done = ( current_mol >= tot_nmol );
891	>	#ifdef IS_MPI
892	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
893	>	MPIcheckPoint();
894	>	#endif // is_mpi
895	>	}
896
1044	–	if( !done && n_per_extra > 1 ){
1045	–	makeElement( i * cellx + 0.5 * cellx,
1046	–	j * celly + 0.5 * celly,
1047	–	k * cellz );
1048	–	done = ( current_mol >= tot_nmol );
1049	–	}
897
898	<	if( !done && n_per_extra > 2){
899	<	makeElement( i * cellx,
1053	<	j * celly + 0.5 * celly,
1054	<	k * cellz + 0.5 * cellz );
1055	<	done = ( current_mol >= tot_nmol );
1056	<	}
898	>	void SimSetup::makeOutNames(void){
899	>	int k;
900
901	<	if( !done && n_per_extra > 3){
902	<	makeElement( i * cellx + 0.5 * cellx,
903	<	j * celly,
904	<	k * cellz + 0.5 * cellz );
905	<	done = ( current_mol >= tot_nmol );
906	<	}
907	<	}
901	>
902	>	for (k = 0; k < nInfo; k++){
903	>	#ifdef IS_MPI
904	>	if (worldRank == 0){
905	>	#endif // is_mpi
906	>
907	>	if (globals->haveFinalConfig()){
908	>	strcpy(info[k].finalName, globals->getFinalConfig());
909		}
910	<	}
911	<	}
910	>	else{
911	>	strcpy(info[k].finalName, inFileName);
912	>	char* endTest;
913	>	int nameLength = strlen(info[k].finalName);
914	>	endTest = &(info[k].finalName[nameLength - 5]);
915	>	if (!strcmp(endTest, ".bass")){
916	>	strcpy(endTest, ".eor");
917	>	}
918	>	else if (!strcmp(endTest, ".BASS")){
919	>	strcpy(endTest, ".eor");
920	>	}
921	>	else{
922	>	endTest = &(info[k].finalName[nameLength - 4]);
923	>	if (!strcmp(endTest, ".bss")){
924	>	strcpy(endTest, ".eor");
925	>	}
926	>	else if (!strcmp(endTest, ".mdl")){
927	>	strcpy(endTest, ".eor");
928	>	}
929	>	else{
930	>	strcat(info[k].finalName, ".eor");
931	>	}
932	>	}
933	>	}
934
935	+	// make the sample and status out names
936
937	<	for( i=0; i<simnfo->n_atoms; i++ ){
938	<	simnfo->atoms[i]->set_vx( 0.0 );
939	<	simnfo->atoms[i]->set_vy( 0.0 );
940	<	simnfo->atoms[i]->set_vz( 0.0 );
937	>	strcpy(info[k].sampleName, inFileName);
938	>	char* endTest;
939	>	int nameLength = strlen(info[k].sampleName);
940	>	endTest = &(info[k].sampleName[nameLength - 5]);
941	>	if (!strcmp(endTest, ".bass")){
942	>	strcpy(endTest, ".dump");
943	>	}
944	>	else if (!strcmp(endTest, ".BASS")){
945	>	strcpy(endTest, ".dump");
946	>	}
947	>	else{
948	>	endTest = &(info[k].sampleName[nameLength - 4]);
949	>	if (!strcmp(endTest, ".bss")){
950	>	strcpy(endTest, ".dump");
951	>	}
952	>	else if (!strcmp(endTest, ".mdl")){
953	>	strcpy(endTest, ".dump");
954	>	}
955	>	else{
956	>	strcat(info[k].sampleName, ".dump");
957	>	}
958	>	}
959	>
960	>	strcpy(info[k].statusName, inFileName);
961	>	nameLength = strlen(info[k].statusName);
962	>	endTest = &(info[k].statusName[nameLength - 5]);
963	>	if (!strcmp(endTest, ".bass")){
964	>	strcpy(endTest, ".stat");
965	>	}
966	>	else if (!strcmp(endTest, ".BASS")){
967	>	strcpy(endTest, ".stat");
968	>	}
969	>	else{
970	>	endTest = &(info[k].statusName[nameLength - 4]);
971	>	if (!strcmp(endTest, ".bss")){
972	>	strcpy(endTest, ".stat");
973	>	}
974	>	else if (!strcmp(endTest, ".mdl")){
975	>	strcpy(endTest, ".stat");
976	>	}
977	>	else{
978	>	strcat(info[k].statusName, ".stat");
979	>	}
980	>	}
981	>
982	>	#ifdef IS_MPI
983	>
984	>	}
985	>	#endif // is_mpi
986		}
987		}
988
1077	–	void SimSetup::makeElement( double x, double y, double z ){
989
990	<	int k;
991	<	AtomStamp* current_atom;
1081	<	DirectionalAtom* dAtom;
1082	<	double rotMat[3][3];
990	>	void SimSetup::sysObjectsCreation(void){
991	>	int i, k;
992
993	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
993	>	// create the forceField
994
995	<	current_atom = comp_stamps[current_comp]->getAtom( k );
996	<	if( !current_atom->havePosition() ){
997	<	sprintf( painCave.errMsg,
998	<	"SimSetup:initFromBass error.\n"
999	<	"\tComponent %s, atom %s does not have a position specified.\n"
1000	<	"\tThe initialization routine is unable to give a start"
1001	<	" position.\n",
1002	<	comp_stamps[current_comp]->getID(),
1003	<	current_atom->getType() );
995	>	createFF();
996	>
997	>	// extract componentList
998	>
999	>	compList();
1000	>
1001	>	// calc the number of atoms, bond, bends, and torsions
1002	>
1003	>	calcSysValues();
1004	>
1005	>	#ifdef IS_MPI
1006	>	// divide the molecules among the processors
1007	>
1008	>	mpiMolDivide();
1009	>	#endif //is_mpi
1010	>
1011	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1012	>
1013	>	makeSysArrays();
1014	>
1015	>	// make and initialize the molecules (all but atomic coordinates)
1016	>
1017	>	makeMolecules();
1018	>
1019	>	for (k = 0; k < nInfo; k++){
1020	>	info[k].identArray = new int[info[k].n_atoms];
1021	>	for (i = 0; i < info[k].n_atoms; i++){
1022	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1023	>	}
1024	>	}
1025	>	}
1026	>
1027	>
1028	>	void SimSetup::createFF(void){
1029	>	switch (ffCase){
1030	>	case FF_DUFF:
1031	>	the_ff = new DUFF();
1032	>	break;
1033	>
1034	>	case FF_LJ:
1035	>	the_ff = new LJFF();
1036	>	break;
1037	>
1038	>	case FF_EAM:
1039	>	the_ff = new EAM_FF();
1040	>	break;
1041	>
1042	>	default:
1043	>	sprintf(painCave.errMsg,
1044	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1045		painCave.isFatal = 1;
1046		simError();
1047	+	}
1048	+
1049	+	#ifdef IS_MPI
1050	+	strcpy(checkPointMsg, "ForceField creation successful");
1051	+	MPIcheckPoint();
1052	+	#endif // is_mpi
1053	+	}
1054	+
1055	+
1056	+	void SimSetup::compList(void){
1057	+	int i;
1058	+	char* id;
1059	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1060	+	LinkedMolStamp* currentStamp = NULL;
1061	+	comp_stamps = new MoleculeStamp * [n_components];
1062	+
1063	+	// make an array of molecule stamps that match the components used.
1064	+	// also extract the used stamps out into a separate linked list
1065	+
1066	+	for (i = 0; i < nInfo; i++){
1067	+	info[i].nComponents = n_components;
1068	+	info[i].componentsNmol = components_nmol;
1069	+	info[i].compStamps = comp_stamps;
1070	+	info[i].headStamp = headStamp;
1071	+	}
1072	+
1073	+
1074	+	for (i = 0; i < n_components; i++){
1075	+	id = the_components[i]->getType();
1076	+	comp_stamps[i] = NULL;
1077	+
1078	+	// check to make sure the component isn't already in the list
1079	+
1080	+	comp_stamps[i] = headStamp->match(id);
1081	+	if (comp_stamps[i] == NULL){
1082	+	// extract the component from the list;
1083	+
1084	+	currentStamp = stamps->extractMolStamp(id);
1085	+	if (currentStamp == NULL){
1086	+	sprintf(painCave.errMsg,
1087	+	"SimSetup error: Component \"%s\" was not found in the "
1088	+	"list of declared molecules\n",
1089	+	id);
1090	+	painCave.isFatal = 1;
1091	+	simError();
1092	+	}
1093	+
1094	+	headStamp->add(currentStamp);
1095	+	comp_stamps[i] = headStamp->match(id);
1096		}
1097	+	}
1098
1099	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1100	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1101	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1099	>	#ifdef IS_MPI
1100	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1101	>	MPIcheckPoint();
1102	>	#endif // is_mpi
1103	>	}
1104
1105	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1105	>	void SimSetup::calcSysValues(void){
1106	>	int i;
1107
1108	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1108	>	int* molMembershipArray;
1109
1110	<	rotMat[0][0] = 1.0;
1111	<	rotMat[0][1] = 0.0;
1112	<	rotMat[0][2] = 0.0;
1110	>	tot_atoms = 0;
1111	>	tot_bonds = 0;
1112	>	tot_bends = 0;
1113	>	tot_torsions = 0;
1114	>	for (i = 0; i < n_components; i++){
1115	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1116	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1117	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1118	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1119	>	}
1120
1121	<	rotMat[1][0] = 0.0;
1122	<	rotMat[1][1] = 1.0;
1113	<	rotMat[1][2] = 0.0;
1121	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1122	>	molMembershipArray = new int[tot_atoms];
1123
1124	<	rotMat[2][0] = 0.0;
1125	<	rotMat[2][1] = 0.0;
1126	<	rotMat[2][2] = 1.0;
1124	>	for (i = 0; i < nInfo; i++){
1125	>	info[i].n_atoms = tot_atoms;
1126	>	info[i].n_bonds = tot_bonds;
1127	>	info[i].n_bends = tot_bends;
1128	>	info[i].n_torsions = tot_torsions;
1129	>	info[i].n_SRI = tot_SRI;
1130	>	info[i].n_mol = tot_nmol;
1131
1132	<	dAtom->setA( rotMat );
1132	>	info[i].molMembershipArray = molMembershipArray;
1133	>	}
1134	>	}
1135	>
1136	>	#ifdef IS_MPI
1137	>
1138	>	void SimSetup::mpiMolDivide(void){
1139	>	int i, j, k;
1140	>	int localMol, allMol;
1141	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1142	>
1143	>	mpiSim = new mpiSimulation(info);
1144	>
1145	>	globalIndex = mpiSim->divideLabor();
1146	>
1147	>	// set up the local variables
1148	>
1149	>	mol2proc = mpiSim->getMolToProcMap();
1150	>	molCompType = mpiSim->getMolComponentType();
1151	>
1152	>	allMol = 0;
1153	>	localMol = 0;
1154	>	local_atoms = 0;
1155	>	local_bonds = 0;
1156	>	local_bends = 0;
1157	>	local_torsions = 0;
1158	>	globalAtomIndex = 0;
1159	>
1160	>
1161	>	for (i = 0; i < n_components; i++){
1162	>	for (j = 0; j < components_nmol[i]; j++){
1163	>	if (mol2proc[allMol] == worldRank){
1164	>	local_atoms += comp_stamps[i]->getNAtoms();
1165	>	local_bonds += comp_stamps[i]->getNBonds();
1166	>	local_bends += comp_stamps[i]->getNBends();
1167	>	local_torsions += comp_stamps[i]->getNTorsions();
1168	>	localMol++;
1169	>	}
1170	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1171	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1172	>	globalAtomIndex++;
1173	>	}
1174	>
1175	>	allMol++;
1176		}
1177	+	}
1178	+	local_SRI = local_bonds + local_bends + local_torsions;
1179
1180	<	current_atom_ndx++;
1180	>	info[0].n_atoms = mpiSim->getMyNlocal();
1181	>
1182	>	if (local_atoms != info[0].n_atoms){
1183	>	sprintf(painCave.errMsg,
1184	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1185	>	" localAtom (%d) are not equal.\n",
1186	>	info[0].n_atoms, local_atoms);
1187	>	painCave.isFatal = 1;
1188	>	simError();
1189		}
1190
1191	<	current_mol++;
1192	<	current_comp_mol++;
1191	>	info[0].n_bonds = local_bonds;
1192	>	info[0].n_bends = local_bends;
1193	>	info[0].n_torsions = local_torsions;
1194	>	info[0].n_SRI = local_SRI;
1195	>	info[0].n_mol = localMol;
1196
1197	<	if( current_comp_mol >= components_nmol[current_comp] ){
1197	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1198	>	MPIcheckPoint();
1199	>	}
1200
1201	<	current_comp_mol = 0;
1202	<	current_comp++;
1201	>	#endif // is_mpi
1202	>
1203	>
1204	>	void SimSetup::makeSysArrays(void){
1205	>
1206	>	#ifndef IS_MPI
1207	>	int k, j;
1208	>	#endif // is_mpi
1209	>	int i, l;
1210	>
1211	>	Atom** the_atoms;
1212	>	Molecule* the_molecules;
1213	>	Exclude** the_excludes;
1214	>
1215	>
1216	>	for (l = 0; l < nInfo; l++){
1217	>	// create the atom and short range interaction arrays
1218	>
1219	>	the_atoms = new Atom * [info[l].n_atoms];
1220	>	the_molecules = new Molecule[info[l].n_mol];
1221	>	int molIndex;
1222	>
1223	>	// initialize the molecule's stampID's
1224	>
1225	>	#ifdef IS_MPI
1226	>
1227	>
1228	>	molIndex = 0;
1229	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1230	>	if (mol2proc[i] == worldRank){
1231	>	the_molecules[molIndex].setStampID(molCompType[i]);
1232	>	the_molecules[molIndex].setMyIndex(molIndex);
1233	>	the_molecules[molIndex].setGlobalIndex(i);
1234	>	molIndex++;
1235	>	}
1236	>	}
1237	>
1238	>	#else // is_mpi
1239	>
1240	>	molIndex = 0;
1241	>	globalAtomIndex = 0;
1242	>	for (i = 0; i < n_components; i++){
1243	>	for (j = 0; j < components_nmol[i]; j++){
1244	>	the_molecules[molIndex].setStampID(i);
1245	>	the_molecules[molIndex].setMyIndex(molIndex);
1246	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1247	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1248	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1249	>	globalAtomIndex++;
1250	>	}
1251	>	molIndex++;
1252	>	}
1253	>	}
1254	>
1255	>
1256	>	#endif // is_mpi
1257	>
1258	>
1259	>	if (info[l].n_SRI){
1260	>	Exclude::createArray(info[l].n_SRI);
1261	>	the_excludes = new Exclude * [info[l].n_SRI];
1262	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1263	>	the_excludes[ex] = new Exclude(ex);
1264	>	}
1265	>	info[l].globalExcludes = new int;
1266	>	info[l].n_exclude = info[l].n_SRI;
1267	>	}
1268	>	else{
1269	>	Exclude::createArray(1);
1270	>	the_excludes = new Exclude * ;
1271	>	the_excludes[0] = new Exclude(0);
1272	>	the_excludes[0]->setPair(0, 0);
1273	>	info[l].globalExcludes = new int;
1274	>	info[l].globalExcludes[0] = 0;
1275	>	info[l].n_exclude = 0;
1276	>	}
1277	>
1278	>	// set the arrays into the SimInfo object
1279	>
1280	>	info[l].atoms = the_atoms;
1281	>	info[l].molecules = the_molecules;
1282	>	info[l].nGlobalExcludes = 0;
1283	>	info[l].excludes = the_excludes;
1284	>
1285	>	the_ff->setSimInfo(info);
1286	>	}
1287	>	}
1288	>
1289	>	void SimSetup::makeIntegrator(void){
1290	>	int k;
1291	>
1292	>	NVE<RealIntegrator>* myNVE = NULL;
1293	>	NVT<RealIntegrator>* myNVT = NULL;
1294	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1295	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1296	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1297	>
1298	>	for (k = 0; k < nInfo; k++){
1299	>	switch (ensembleCase){
1300	>	case NVE_ENS:
1301	>	if (globals->haveZconstraints()){
1302	>	setupZConstraint(info[k]);
1303	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1304	>	}
1305	>	else{
1306	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1307	>	}
1308	>
1309	>	info->the_integrator = myNVE;
1310	>	break;
1311	>
1312	>	case NVT_ENS:
1313	>	if (globals->haveZconstraints()){
1314	>	setupZConstraint(info[k]);
1315	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1316	>	}
1317	>	else
1318	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1319	>
1320	>	myNVT->setTargetTemp(globals->getTargetTemp());
1321	>
1322	>	if (globals->haveTauThermostat())
1323	>	myNVT->setTauThermostat(globals->getTauThermostat());
1324	>	else{
1325	>	sprintf(painCave.errMsg,
1326	>	"SimSetup error: If you use the NVT\n"
1327	>	"    ensemble, you must set tauThermostat.\n");
1328	>	painCave.isFatal = 1;
1329	>	simError();
1330	>	}
1331	>
1332	>	info->the_integrator = myNVT;
1333	>	break;
1334	>
1335	>	case NPTi_ENS:
1336	>	if (globals->haveZconstraints()){
1337	>	setupZConstraint(info[k]);
1338	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1339	>	}
1340	>	else
1341	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1342	>
1343	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1344	>
1345	>	if (globals->haveTargetPressure())
1346	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1347	>	else{
1348	>	sprintf(painCave.errMsg,
1349	>	"SimSetup error: If you use a constant pressure\n"
1350	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1351	>	painCave.isFatal = 1;
1352	>	simError();
1353	>	}
1354	>
1355	>	if (globals->haveTauThermostat())
1356	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1357	>	else{
1358	>	sprintf(painCave.errMsg,
1359	>	"SimSetup error: If you use an NPT\n"
1360	>	"    ensemble, you must set tauThermostat.\n");
1361	>	painCave.isFatal = 1;
1362	>	simError();
1363	>	}
1364	>
1365	>	if (globals->haveTauBarostat())
1366	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1367	>	else{
1368	>	sprintf(painCave.errMsg,
1369	>	"SimSetup error: If you use an NPT\n"
1370	>	"    ensemble, you must set tauBarostat.\n");
1371	>	painCave.isFatal = 1;
1372	>	simError();
1373	>	}
1374	>
1375	>	info->the_integrator = myNPTi;
1376	>	break;
1377	>
1378	>	case NPTf_ENS:
1379	>	if (globals->haveZconstraints()){
1380	>	setupZConstraint(info[k]);
1381	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1382	>	}
1383	>	else
1384	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1385	>
1386	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1387	>
1388	>	if (globals->haveTargetPressure())
1389	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1390	>	else{
1391	>	sprintf(painCave.errMsg,
1392	>	"SimSetup error: If you use a constant pressure\n"
1393	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1394	>	painCave.isFatal = 1;
1395	>	simError();
1396	>	}
1397	>
1398	>	if (globals->haveTauThermostat())
1399	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1400	>
1401	>	else{
1402	>	sprintf(painCave.errMsg,
1403	>	"SimSetup error: If you use an NPT\n"
1404	>	"    ensemble, you must set tauThermostat.\n");
1405	>	painCave.isFatal = 1;
1406	>	simError();
1407	>	}
1408	>
1409	>	if (globals->haveTauBarostat())
1410	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1411	>
1412	>	else{
1413	>	sprintf(painCave.errMsg,
1414	>	"SimSetup error: If you use an NPT\n"
1415	>	"    ensemble, you must set tauBarostat.\n");
1416	>	painCave.isFatal = 1;
1417	>	simError();
1418	>	}
1419	>
1420	>	info->the_integrator = myNPTf;
1421	>	break;
1422	>
1423	>	case NPTxyz_ENS:
1424	>	if (globals->haveZconstraints()){
1425	>	setupZConstraint(info[k]);
1426	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1427	>	}
1428	>	else
1429	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1430	>
1431	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1432	>
1433	>	if (globals->haveTargetPressure())
1434	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1435	>	else{
1436	>	sprintf(painCave.errMsg,
1437	>	"SimSetup error: If you use a constant pressure\n"
1438	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1439	>	painCave.isFatal = 1;
1440	>	simError();
1441	>	}
1442	>
1443	>	if (globals->haveTauThermostat())
1444	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1445	>	else{
1446	>	sprintf(painCave.errMsg,
1447	>	"SimSetup error: If you use an NPT\n"
1448	>	"    ensemble, you must set tauThermostat.\n");
1449	>	painCave.isFatal = 1;
1450	>	simError();
1451	>	}
1452	>
1453	>	if (globals->haveTauBarostat())
1454	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1455	>	else{
1456	>	sprintf(painCave.errMsg,
1457	>	"SimSetup error: If you use an NPT\n"
1458	>	"    ensemble, you must set tauBarostat.\n");
1459	>	painCave.isFatal = 1;
1460	>	simError();
1461	>	}
1462	>
1463	>	info->the_integrator = myNPTxyz;
1464	>	break;
1465	>
1466	>	default:
1467	>	sprintf(painCave.errMsg,
1468	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1469	>	painCave.isFatal = 1;
1470	>	simError();
1471	>	}
1472		}
1473		}
1474	+
1475	+	void SimSetup::initFortran(void){
1476	+	info[0].refreshSim();
1477	+
1478	+	if (!strcmp(info[0].mixingRule, "standard")){
1479	+	the_ff->initForceField(LB_MIXING_RULE);
1480	+	}
1481	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1482	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1483	+	}
1484	+	else{
1485	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1486	+	info[0].mixingRule);
1487	+	painCave.isFatal = 1;
1488	+	simError();
1489	+	}
1490	+
1491	+
1492	+	#ifdef IS_MPI
1493	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1494	+	MPIcheckPoint();
1495	+	#endif // is_mpi
1496	+	}
1497	+
1498	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1499	+	int nZConstraints;
1500	+	ZconStamp** zconStamp;
1501	+
1502	+	if (globals->haveZconstraintTime()){
1503	+	//add sample time of z-constraint  into SimInfo's property list
1504	+	DoubleData* zconsTimeProp = new DoubleData();
1505	+	zconsTimeProp->setID(ZCONSTIME_ID);
1506	+	zconsTimeProp->setData(globals->getZconsTime());
1507	+	theInfo.addProperty(zconsTimeProp);
1508	+	}
1509	+	else{
1510	+	sprintf(painCave.errMsg,
1511	+	"ZConstraint error: If you use an ZConstraint\n"
1512	+	" , you must set sample time.\n");
1513	+	painCave.isFatal = 1;
1514	+	simError();
1515	+	}
1516	+
1517	+	//push zconsTol into siminfo, if user does not specify
1518	+	//value for zconsTol, a default value will be used
1519	+	DoubleData* zconsTol = new DoubleData();
1520	+	zconsTol->setID(ZCONSTOL_ID);
1521	+	if (globals->haveZconsTol()){
1522	+	zconsTol->setData(globals->getZconsTol());
1523	+	}
1524	+	else{
1525	+	double defaultZConsTol = 0.01;
1526	+	sprintf(painCave.errMsg,
1527	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1528	+	" , default value %f is used.\n",
1529	+	defaultZConsTol);
1530	+	painCave.isFatal = 0;
1531	+	simError();
1532	+
1533	+	zconsTol->setData(defaultZConsTol);
1534	+	}
1535	+	theInfo.addProperty(zconsTol);
1536	+
1537	+	//set Force Subtraction Policy
1538	+	StringData* zconsForcePolicy = new StringData();
1539	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1540	+
1541	+	if (globals->haveZconsForcePolicy()){
1542	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1543	+	}
1544	+	else{
1545	+	sprintf(painCave.errMsg,
1546	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1547	+	"PolicyByMass is used\n");
1548	+	painCave.isFatal = 0;
1549	+	simError();
1550	+	zconsForcePolicy->setData("BYMASS");
1551	+	}
1552	+
1553	+	theInfo.addProperty(zconsForcePolicy);
1554	+
1555	+	//Determine the name of ouput file and add it into SimInfo's property list
1556	+	//Be careful, do not use inFileName, since it is a pointer which
1557	+	//point to a string at master node, and slave nodes do not contain that string
1558	+
1559	+	string zconsOutput(theInfo.finalName);
1560	+
1561	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1562	+
1563	+	StringData* zconsFilename = new StringData();
1564	+	zconsFilename->setID(ZCONSFILENAME_ID);
1565	+	zconsFilename->setData(zconsOutput);
1566	+
1567	+	theInfo.addProperty(zconsFilename);
1568	+
1569	+	//setup index, pos and other parameters of z-constraint molecules
1570	+	nZConstraints = globals->getNzConstraints();
1571	+	theInfo.nZconstraints = nZConstraints;
1572	+
1573	+	zconStamp = globals->getZconStamp();
1574	+	ZConsParaItem tempParaItem;
1575	+
1576	+	ZConsParaData* zconsParaData = new ZConsParaData();
1577	+	zconsParaData->setID(ZCONSPARADATA_ID);
1578	+
1579	+	for (int i = 0; i < nZConstraints; i++){
1580	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1581	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1582	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1583	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1584	+
1585	+	zconsParaData->addItem(tempParaItem);
1586	+	}
1587	+
1588	+	//check the uniqueness of index
1589	+	if(!zconsParaData->isIndexUnique()){
1590	+	sprintf(painCave.errMsg,
1591	+	"ZConstraint Error: molIndex is not unique\n");
1592	+	painCave.isFatal = 1;
1593	+	simError();
1594	+	}
1595	+
1596	+	//sort the parameters by index of molecules
1597	+	zconsParaData->sortByIndex();
1598	+
1599	+	//push data into siminfo, therefore, we can retrieve later
1600	+	theInfo.addProperty(zconsParaData);
1601	+	}

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